[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

Fabio Affinito wrote:
> On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
>>
>>
>> Fabio Affinito wrote:
>>> This is the mdrun output:
>>>
>>> Initializing Domain Decomposition on 4096 nodes
>>> Dynamic load balancing: auto
>>> Will sort the charge groups at every domain (re)decomposition
>>> Initial maximum inter charge-group distances:
>>> two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705
>>> multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704
>>> Minimum cell size due to bonded interactions: 33.035 nm
>>> Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
>>> 1.139 nm
>>> Estimated maximum distance required for P-LINCS: 1.139 nm
>>> Guess for relative PME load: 0.43
>>> Will use 2400 particle-particle and 1696 PME only nodes
>>> This is a guess, check the performance at the end of the log file
>>> Using 1696 separate PME nodes
>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>> Optimizing the DD grid for 2400 cells with a minimum initial size of
>>> 41.293 nm
>>> The maximum allowed number of cells is: X 0 Y 0 Z 0
>>>
>>> -------------------------------------------------------
>>> Program mdrun_mpi_bg, VERSION 4.5.4
>>> Source code file: domdec.c, line: 6438
>>>
>>> Fatal error:
>>> There is no domain decomposition for 2400 nodes that is compatible
>>> with the given box and a minimum cell size of 41.2932 nm
>>> Change the number of nodes or mdrun option -rdd or -dds
>>> Look in the log file for details on the domain decomposition
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>>
>>
>> This is bizarre. Did you fix the periodicity of the original coordinate
>> file (conf_start.gro) and rebuild the system, or did you try to run
>> trjconv on the replicated system? The former is the correct approach.
>>
>> -Justin
>>
> This is what I did (in the chronological order):
> 
> 1) trjconv -f conf_start.gro -o conf_whole.gro -pbc whole

Presumably in conjunction with a .tpr file, in order for this to work?

> 2) genconf -f conf_whole.gro -o out.gro -nbox 2 2 1
> 3) i modified the topol.top (modifying the number of molecules)
> 4) grompp -f grompp.mdp -c out.gro -p topol.top  -maxwarn 3

What are the warnings you are trying to circumvent?  Please provide the full 
grompp output.  I can think of a few other possibilities for the source of your 
problem, but I do not want to venture idle guesswork without seeing all of the 
warnings you've got.

-Justin

> 5) launched mdrun
> 
> Fabio

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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